Mycosis fungoides (MF) is a type of cutaneous T cell lymphoma (CTCL) characterized at early stages by patches or raised plaques on the skin surface. A fraction of MF cases progress to form tumors and systemic involvement in the advanced stages of disease, unfortunately progression follows no predictable or clear course. Identification of cases likely to progress is of great clinical significance to patients and the physicians who treat them, as advanced stage is associated with marked decreases in median survival times from over twenty years to less than five. Attempts to identify prognostic biomarkers for the early prediction of cases that may progress have long been hindered by the technical challenges in efficiently identifying and isolating neoplastic cells from early lesions prior to the accumulation of numerous chromosome abnormalities. Potential biomarkers identified in advanced stage disease to circumvent this problem have proven unreliable in their ability to similarly identify early stage lesions that have yet to progress. To surmount these challenges we will use information gained from the high throughput sequence analysis of T cell receptor rearrangements to generate MF clone-specific DNA probes for in situ hybridization based on the unique CDR3 rearrangements of the neoplastic cells. Laser capture microdissection will be performed on tissue from early patch/plaque stage lesions of mycosis fungoides with the aid of these probes to specifically isolate MF cells. Because only 10- 20% of patients with mycosis fungoides develop progressive disease, we have limited our test population to early biopsies from patch/plaque stage lesions retrospectively identified to come from patients proven to have later developed progressive disease. These samples will be compared with a cohort of biopsies from 'non- progressors' who have carried a confirmed diagnosis of MF for over 10 years without progression. Isolated neoplastic cells will be used for genomic analysis to study differential gene expression and chromosomal imbalances between progressors and non-progressors in order to identify putative biomarkers. Upon completion of this project we hope to have identified better prognostic markers for patients destined to develop progressive disease, which will influence treatment approaches. In addition, we will have gained new insight into the pathogenesis of mycosis fungoides, possibly opening unanticipated new avenues to novel therapeutic approaches.